chrigu,
I have the same problem and I submitted an SR on this and Altera has acknowledged that it is a bug. This bug will be fixed in version 12.1 due out this fall/early winter. The workaround is to add all the files once to the custom component and then only update the component editing the _hw.tcl file manually.
I found another issue with the component UI in qsys and that as well has been submitted and they can verify that it is a problem. If you add a .qip file to the fileset of a custom component once you generate the system in qsys and then compile it in Quartus. Quartus will not find the files that the .qip file points to since it relies on relative paths to where the .qip file is located and during qsys generation the .qip file is copied to a qsys system directory.
/Boris